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Proteomics and Metabonomics for Personalised Medicine

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: closed (30 June 2022) | Viewed by 11651

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Special Issue Editors

Prof. Dr. Andrea Urbani

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Guest Editor

Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
Interests: proteomics; metabonomics; small molecules; mass spectrometry; personalized medicine; drug discovery

Dr. Federica Iavarone

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Guest Editor

1. Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, 20123 Rome, Italy 2. Fondazione Policlinico Universitario IRCCS “A. Gemelli”, 00168 Rome, Italy
Interests: human proteomics; metabonomics; small molecules; mass spectrometry; biomarkers

Special Issue Information

Dear Colleagues,

A number of physiological and pathological conditions are characterized by dynamic remodeling of the proteome and with a deep modification in the concentration of metabolites in the organism.

Molecular phenotyping, in particular proteomics and metabolomics, offers great promise in this field. Indeed, on one hand, they lead to the discovery of new, biologically and clinically relevant biomarkers, for personalizing preventive and therapeutic interventions. On the other hand, they contribute new knowledge in terms of molecular mechanisms. Furthermore, the combined integrative genomics approaches with proteo-metabolomic investigations are developing rapidly and are particularly relevant in the understanding of several pathologies.

For this Special Issue, we invite authors to contribute original research articles, method papers, as well as review articles that will address recent developments in the area of proteomics and metabolomics.

Potential topics include but are not limited to the following:

Reference standards and intervals for clinical proteomics;
Integrative genomics on the verge of proteomics and metabolomics;
Novel mass spectrometry methods for clinical practice;
Bioinformatics for the analysis of proteomics and metabolomics data;
Molecular protein networks;
Targeted, untargeted metabolomics;
II order molecular cybernetics mechanisms.

Prof. Dr. Andrea Urbani
Prof. Dr. Federica Iavarone
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

Personalized medicine
Molecular phenotyping
Proteogenomics
Systems biology and medicine
Mass spectrometry

Published Papers (3 papers)

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Research

15 pages, 2062 KiB

Open AccessArticle

Effects of l-Arginine Plus Vitamin C Supplementation on l-Arginine Metabolism in Adults with Long COVID: Secondary Analysis of a Randomized Clinical Trial

by Riccardo Calvani, Jacopo Gervasoni, Anna Picca, Francesca Ciciarello, Vincenzo Galluzzo, Hélio José Coelho-Júnior, Clara Di Mario, Elisa Gremese, Sara Lomuscio, Anna Maria Paglionico, Lavinia Santucci, Barbara Tolusso, Andrea Urbani, Federico Marini, Emanuele Marzetti, Francesco Landi and Matteo Tosato

Int. J. Mol. Sci. 2023, 24(6), 5078; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24065078 - 07 Mar 2023

Cited by 2 | Viewed by 5104

Abstract

Altered l-arginine metabolism has been described in patients with COVID-19 and has been associated with immune and vascular dysfunction. In the present investigation, we determined the serum concentrations of l-arginine, citrulline, ornithine, monomethyl-l-arginine (MMA), and symmetric and asymmetric dimethylarginine (SDMA, ADMA) in adults with long COVID at baseline and after 28-days of l-arginine plus vitamin C or placebo supplementation enrolled in a randomized clinical trial, compared with a group of adults without previous history of SARS-CoV-2-infection. l-arginine-derived markers of nitric oxide (NO) bioavailability (i.e., l-arginine/ADMA, l-arginine/citrulline+ornithine, and l-arginine/ornithine) were also assayed. Partial least squares discriminant analysis (PLS–DA) models were built to characterize systemic l-arginine metabolism and assess the effects of the supplementation. PLS–DA allowed discrimination of participants with long COVID from healthy controls with 80.2 ± 3.0% accuracy. Lower markers of NO bioavailability were found in participants with long COVID. After 28 days of l-arginine plus vitamin C supplementation, serum l-arginine concentrations and l-arginine/ADMA increased significantly compared with placebo. This supplement may therefore be proposed as a remedy to increase NO bioavailability in people with long COVID. Full article

(This article belongs to the Special Issue Proteomics and Metabonomics for Personalised Medicine)

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21 pages, 3055 KiB

Open AccessArticle

Top-Down Proteomics Detection of Potential Salivary Biomarkers for Autoimmune Liver Diseases Classification

by Alessandra Olianas, Giulia Guadalupi, Tiziana Cabras, Cristina Contini, Simone Serrao, Federica Iavarone, Massimo Castagnola, Irene Messana, Simona Onali, Luchino Chessa, Giacomo Diaz and Barbara Manconi

Int. J. Mol. Sci. 2023, 24(2), 959; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24020959 - 04 Jan 2023

Cited by 7 | Viewed by 2280

Abstract

(1) Autoimmune hepatitis (AIH) and primary biliary cholangitis (PBC) are autoimmune liver diseases characterized by chronic hepatic inflammation and progressive liver fibrosis. The possible use of saliva as a diagnostic tool has been explored in several oral and systemic diseases. The use of proteomics for personalized medicine is a rapidly emerging field. (2) Salivary proteomic data of 36 healthy controls (HCs), 36 AIH and 36 PBC patients, obtained by liquid chromatography/mass spectrometry top-down pipeline, were analyzed by multiple Mann—Whitney test, Kendall correlation, Random Forest (RF) analysis and Linear Discriminant Analysis (LDA); (3) Mann—Whitney tests provided indications on the panel of differentially expressed salivary proteins and peptides, namely cystatin A, statherin, histatin 3, histatin 5 and histatin 6, which were elevated in AIH patients with respect to both HCs and PBC patients, while S100A12, S100A9 short, cystatin S1, S2, SN and C showed varied levels in PBC with respect to HCs and/or AIH patients. RF analysis evidenced a panel of salivary proteins/peptides able to classify with good accuracy PBC vs. HCs (83.3%), AIH vs. HCs (79.9%) and PBC vs. AIH (80.2%); (4) RF appears to be an attractive machine-learning tool suited for classification of AIH and PBC based on their different salivary proteomic profiles. Full article

(This article belongs to the Special Issue Proteomics and Metabonomics for Personalised Medicine)

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Graphical abstract

23 pages, 4376 KiB

Open AccessArticle

Multi-Omics Approach to Elucidate Cerebrospinal Fluid Changes in Dogs with Intervertebral Disc Herniation

by Anita Horvatić, Andrea Gelemanović, Boris Pirkić, Ozren Smolec, Blanka Beer Ljubić, Ivana Rubić, Peter David Eckersall, Vladimir Mrljak, Mark McLaughlin, Marko Samardžija and Marija Lipar

Int. J. Mol. Sci. 2021, 22(21), 11678; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222111678 - 28 Oct 2021

Cited by 4 | Viewed by 3029

Abstract

Herniation of the intervertebral disc (IVDH) is the most common cause of neurological and intervertebral disc degeneration-related diseases. Since the disc starts to degenerate before it can be observed by currently available diagnostic methods, there is an urgent need for novel diagnostic approaches. To identify molecular networks and pathways which may play important roles in intervertebral disc herniation, as well as to reveal the potential features which could be useful for monitoring disease progression and prognosis, multi-omics profiling, including high-resolution liquid chromatography-mass spectrometry (LC-MS)-based metabolomics and tandem mass tag (TMT)-based proteomics was performed. Cerebrospinal fluid of nine dogs with IVDH and six healthy controls were used for the analyses, and an additional five IVDH samples were used for proteomic data validation. Furthermore, multi-omics data were integrated to decipher a complex interaction between individual omics layers, leading to an improved prediction model. Together with metabolic pathways related to amino acids and lipid metabolism and coagulation cascades, our integromics prediction model identified the key features in IVDH, namely the proteins follistatin Like 1 (FSTL1), secretogranin V (SCG5), nucleobindin 1 (NUCB1), calcitonin re-ceptor-stimulating peptide 2 precursor (CRSP2) and the metabolites N-acetyl-D-glucosamine and adenine, involved in neuropathic pain, myelination, and neurotransmission and inflammatory response, respectively. Their clinical application is to be further investigated. The utilization of a novel integrative interdisciplinary approach may provide new opportunities to apply innovative diagnostic and monitoring methods as well as improve treatment strategies and personalized care for patients with degenerative spinal disorders. Full article

(This article belongs to the Special Issue Proteomics and Metabonomics for Personalised Medicine)

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